[2024-01-24 13:17:13,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,820] [INFO] DQC Reference Directory: /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference
[2024-01-24 13:17:15,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,136] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d70863e-800d-431d-9032-4a0739e9a37e/GCF_027925445.1_ASM2792544v1_genomic.fna.gz | prodigal -d GCF_027925445.1_ASM2792544v1_genomic.fna/cds.fna -a GCF_027925445.1_ASM2792544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:29,366] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:29,366] [INFO] Task started: HMMsearch
[2024-01-24 13:17:29,366] [INFO] Running command: hmmsearch --tblout GCF_027925445.1_ASM2792544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/reference_markers.hmm GCF_027925445.1_ASM2792544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:29,758] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:29,787] [INFO] Found 6/6 markers.
[2024-01-24 13:17:29,842] [INFO] Query marker FASTA was written to GCF_027925445.1_ASM2792544v1_genomic.fna/markers.fasta
[2024-01-24 13:17:29,843] [INFO] Task started: Blastn
[2024-01-24 13:17:29,843] [INFO] Running command: blastn -query GCF_027925445.1_ASM2792544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/reference_markers.fasta -out GCF_027925445.1_ASM2792544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:30,838] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:30,846] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:30,847] [INFO] Target genome list was writen to GCF_027925445.1_ASM2792544v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:30,922] [INFO] Task started: fastANI
[2024-01-24 13:17:30,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d70863e-800d-431d-9032-4a0739e9a37e/GCF_027925445.1_ASM2792544v1_genomic.fna.gz --refList GCF_027925445.1_ASM2792544v1_genomic.fna/target_genomes.txt --output GCF_027925445.1_ASM2792544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:48,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:48,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:48,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:48,158] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:48,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:48,158] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	78.777	489	1571	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	78.6918	504	1571	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	78.5967	448	1571	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	78.5893	449	1571	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	78.5024	442	1571	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	78.441	471	1571	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	78.4397	401	1571	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	78.3617	382	1571	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	78.3098	390	1571	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	78.03	244	1571	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.3236	191	1571	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	76.9039	234	1571	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	76.8814	203	1571	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	76.749	210	1571	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.6945	226	1571	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.6675	195	1571	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.5918	240	1571	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.5713	258	1571	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.5642	225	1571	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	76.4908	205	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:48,160] [INFO] DFAST Taxonomy check result was written to GCF_027925445.1_ASM2792544v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:48,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:48,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:48,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/checkm_data
[2024-01-24 13:17:48,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:48,216] [INFO] Task started: CheckM
[2024-01-24 13:17:48,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027925445.1_ASM2792544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027925445.1_ASM2792544v1_genomic.fna/checkm_input GCF_027925445.1_ASM2792544v1_genomic.fna/checkm_result
[2024-01-24 13:18:31,394] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:31,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,419] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:31,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:31,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027925445.1_ASM2792544v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:31,421] [INFO] Task started: Blastn
[2024-01-24 13:18:31,421] [INFO] Running command: blastn -query GCF_027925445.1_ASM2792544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc345d02b-ccb9-4b12-983a-fdb9e084e758/dqc_reference/reference_markers_gtdb.fasta -out GCF_027925445.1_ASM2792544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:33,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:33,198] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:33,198] [INFO] Target genome list was writen to GCF_027925445.1_ASM2792544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:33,243] [INFO] Task started: fastANI
[2024-01-24 13:18:33,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d70863e-800d-431d-9032-4a0739e9a37e/GCF_027925445.1_ASM2792544v1_genomic.fna.gz --refList GCF_027925445.1_ASM2792544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027925445.1_ASM2792544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:49,908] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:49,922] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:49,923] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002117405.1	s__Methylocystis bryophila	99.9978	1562	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002752655.1	s__Methylosinus trichosporium	78.7453	503	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.98	99.98	1.00	1.00	3	-
GCF_015709455.1	s__Methylosinus sp015709455	78.7354	470	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	78.708	469	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_009936375.1	s__Methylosinus sp009936375	78.7053	467	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	78.6665	477	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	78.5509	448	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004802635.2	s__Methylocystis heyeri	78.5398	450	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963405.1	s__Methylocystis sp003963405	78.5242	420	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003113265.1	s__Methylosinus sporium	78.4886	444	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	98.07	97.36	0.91	0.86	5	-
GCF_000304315.1	s__Methylocystis sp000304315	78.4591	414	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372845.1	s__Methylocystis rosea	78.3516	378	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.62	95.24	0.85	0.83	5	-
GCF_013350005.1	s__Methylocystis sp013350005	78.2868	394	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	96.16	96.16	0.88	0.88	2	-
GCA_016869555.1	s__Methylocystis sp016869555	78.2779	402	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.54	99.54	0.92	0.92	2	-
GCA_003134075.1	s__Methylocystis sp003134075	78.2161	416	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.45	99.32	0.87	0.85	6	-
GCA_003152255.1	s__Methylocystis sp003152255	78.2153	411	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002929055.1	s__Methylocystis sp002929055	78.1914	353	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773555.1	s__Methylocystis sp009773555	78.1743	388	1571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.69	99.47	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:49,924] [INFO] GTDB search result was written to GCF_027925445.1_ASM2792544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:49,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:49,929] [INFO] DFAST_QC result json was written to GCF_027925445.1_ASM2792544v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:49,930] [INFO] DFAST_QC completed!
[2024-01-24 13:18:49,930] [INFO] Total running time: 0h1m36s